From deep TLS validation to ensembles of atomic models built from elemental motions
Category
Published on
Type
posted-content
Author
Alexandre Urzhumtsev and Pavel Afonine and Andrew H Van Benschoten and James Fraser and Paul D Adams
Citation
Urzhumtsev, A. et al., 2015. From deep TLS validation to ensembles of atomic models built from elemental motions. Available at: http://dx.doi.org/10.1101/012930.
Abstract
The widely used Translation Libration Screw (TLS) approximation describes concerted motions of atomic groups in X-ray refinement. TLS refinement often provides a better interpretation of diffraction data and the resulting rigid body motions may subsequently be assigned biochemical significance. In TLS refinement, three matrices (T, L and S) describe harmonic vibration, libration and their correlation. Because these matrices describe specific motions, they impose a number of conditions on their elements. Ignoring these conditions while refining the matrix elements may result in matrices that cannot be interpreted in terms of physically realistic motions. We describe a mathematical framework and the computational tools to analyze refined TLS matrices through their decomposition into descriptors of underlying motions. This allows for straightforward validation and identification of implausible TLS parameters. An algorithm for the generation of structural ensembles that are consistent with given TLS parameters, implemented as a part of the Phenix project, is also described.
DOI
Funding
NSF-STC Biology with X-ray Lasers (NSF-1231306)
